kraken2‐to‐features - bokulich-lab/q2-annotate GitHub Wiki

Convert a Kraken 2 report, which is an annotated NCBI taxonomy tree into generic artifacts for downstream analyses.

For the full description of the action's inputs, outputs and parameters run qiime moshpit kraken2‐to‐features --help in the terminal.

Inputs

• reports (SampleData[Kraken2Reports]): Per-sample Kraken 2 reports.

Outputs

• table (FeatureTable[PresenceAbsence]): A presence/absence table of selected features. The features are not of even ranks, but will be the most specific rank available.
• taxonomy (FeatureData[Taxonomy]): Infra-clade ranks are ignored unless they are strain-level. Missing internal ranks are annotated by their next most specific rank, with the exception of k__Bacteria and k__Archaea which match their domain's name.